/SPARC

Simulation Package for Ab-initio Real-space Calculations

Primary LanguageCGNU General Public License v3.0GPL-3.0

SPARC installation and usage

(1) Brief:

SPARC is an open-source software package for the accurate, effcient, and scalable solution of the Kohn-Sham density functional theory (DFT) problem. The main features of SPARC currently include

  • Isolated systems such as molecules and clusters as well as extended systems such as crystals, surfaces, and wires.
  • Calculation of ground state energy, atomic forces, and stress tensor.
  • Unconstrained collinear magnetization via spin polarized calculations.
  • Structural relaxation and quantum molecular dynamics (QMD).
  • Local and semilocal exchange correlation functionals.
  • ONCV and TM pseudopotentials in psp8 (ABINIT) format.

Additional details regarding the formulation and implementation of SPARC can be found in the accompanying paper.

Users of SPARC are expected to cite the following publication: Q. Xu, A. Sharma, B. Comer, H. Huang, E. Chow, A.J. Medford, J.E. Pask, and P. Suryanarayana, 2020. SPARC: Simulation Package for Ab-initio Real-space Calculations. arXiv preprint arXiv:2005.10431.

(2) Installation:

Prerequisite: C compiler, MPI.

There are several options to compile SPARC, depending on the available external libraries.

  • Option 1 (default): Compile with BLAS and LAPACK.

    • Step 1: Install/Load OpenBLAS/BLAS and LAPACK.

    • Step 2: Change directory to src/ directory, there is an available makefile.

    • Step 3 (optional): Edit makefile. If the BLAS library path and LAPACK library path are not in the search path, edit the BLASROOT and LAPACKROOT variables, and add them to LDFLAGS. If you are using BLAS instead of OpenBLAS, replace all -lopenblas flags with -lblas.

    • Step 4 (optional): To turn on DEBUG mode, set DEBUG_MODE to 1 in the makefile.

    • Step 5: Within the src/ directory, compile the code by

      $ make clean; make

Remark: make sure in the makefile USE_MKL = 0, USE_SCALAPACK = 0, and USE_DP_SUBEIG = 1 for option 1.

  • Option 2 (recommended): Compile with MKL.

    • Step 1: Install/Load MKL.

    • Step 2: Change directory to src/ directory, there is an available makefile.

    • Step 3: Edit makefile . Set USE_MKL to 1 to enable compilation with MKL. If the MKL library path is not in the search path, edit the MKLROOT variable to manually set the MKL path.

    • Step 4 (optional): For the projection/subspace rotation step, to use SPARC routines for matrix data distribution rather than ScaLAPACK (through MKL), set USE_DP_SUBEIG to 1. We found on some machines this option is faster.

    • Step 5 (optional): To turn on DEBUG mode, set DEBUG_MODE to 1 in the makefile .

    • Step 6: Within the src/ directory, compile the code by

      $ make clean; make

Remark: make sure in the makefile USE_MKL = 1 and USE_SCALAPACK = 0 for option 2.

  • Option 3: Compile with BLAS, LAPACK, and ScaLAPACK.

    • Step 1: Install/Load OpenBLAS/BLAS, LAPACK, and ScaLAPACK.

    • Step 2: Change directory to src/ directory, there is an available makefile.

    • Step 3 (optional): Edit makefile. If the BLAS library path, LAPACK library path, and/or ScaLAPACK library path are not in the search path, edit the BLASROOT, LAPACKROOT , and/or SCALAPACKROOT variables accordingly, and add them to LDFLAGS. If you are using BLAS instead of OpenBLAS, replace all -lopenblas flags with -lblas.

    • Step 4 (optional): For the projection/subspace rotation step, to use SPARC routines for matrix data distribution rather than ScaLAPACK, set USE_DP_SUBEIG to 1. We found on some machines this option is faster.

    • Step 5 (optional): To turn on DEBUG mode, set DEBUG_MODE to 1 in the makefile.

    • Step 6: Within the src/ directory, compile the code by

      $ make clean; make

Remark: make sure in the makefile USE_MKL = 0 and USE_SCALAPACK = 1 for option 3.

(3) Input files:

The required input files to run a simulation with SPARC are (with shared names)

(a) ".inpt" -- User options and parameters.

(b) ".ion" -- Atomic information.

It is required that the ".inpt" and ".ion" files are located in the same directory and share the same name. A detailed description of the input options is provided in this document. Examples of input files can be found in the SPARC/tests directory .

In addition, SPARC requires pseudopotential files of psp8 format which can be generated by D. R. Hamann's open-source pseudopotential code ONCVPSP. A large number of accurate and efficient pseudopotentials are already provided within the package. For access to more pseudopotentials, the user is referred to the SG15 ONCV potentials. Using the ONCVPSP input files included in the SG15 ONCV potentials, one can easily convert the SG15 ONCV potentials from upf format to psp8 format. Paths to the pseudopotential files are specified in the ".ion" file.

(4) Execution:

SPARC can be executed in parallel using the mpirun command. Sample PBS script files are available in "SPARC/tests" folder. It is required that the ".inpt" and ".ion" files are located in the same directory and share the same name. For example, to run a simulation with 8 processes with input files as "filename.inpt" and "filename.ion" in the root directory (SPARC/), use the following command:

$ mpirun -np 8 ./lib/sparc -name filename

As an example, one can run a test located in SPARC/tests. First go to SPARC/tests/MeshConvergence/Si8 directory:

$ cd tests/MeshConvergence/Si8

There are a few input files available. Run a DC silicon system with mesh = $0.4$ Bohr by

$ mpirun -np 8 ../../../lib/sparc -name Si8-ONCV-0.4

The result is printed to output file "Si8-ONCV-0.4.out", located in the same directory as the input files. If the file "Si8-ONCV-0.4.out" is already present, the result will be printed to "Si8-ONCV-0.4.out_1" instead. The max number of ".out" files allowed with the same name is 100. Once this number is reached, the result will instead overwrite the "Si8-ONCV-0.4.out" file. One can compare the result with the reference out file named "Si8-ONCV-0.4.refout".

In the tests/quick/ directory, we also provide a sample script file quickrun.sh, which launches four quick tests one by one. To run these quick tests, simply change directory to tests/quick/ directory, and run:

$ chmod +x ./quickrun.sh
$ ./quickrun.sh

(5) Output

Upon successful execution of the sparc code, depending on the calculations performed, some output files will be created in the same location as the input files.

Single point calculations

  • ".out" file

    General information about the test, including input parameters, SCF convergence progress, ground state properties and timing information.

  • ".static" file

    Atomic positions and atomic forces if the user chooses to print these information.

Structural relaxation calculations

  • ".out" file

    See above.

  • ".geopt" file

    Atomic positions and atomic forces for atomic relaxation, cell lengths and stress tensor for volume relaxation, and atomic positions, atomic forces, cell lengths , and stress tensor for full relaxation.

  • ".restart" file

    Information necessary to perform a restarted structural relaxation calculation. Only created if atomic relaxation is performed.

Quantum molecular dynamics (QMD) calculations

  • .out file

    See above.

  • .aimd file

    Atomic positions, atomic velocities, atomic forces, electronic temperature, ionic temperature and total energy for each QMD step.

  • .restart file

    Information necessary to perform a restarted QMD calculation.